Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Ewing, R. M.
Right arrow Articles by Claverie, J.-M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ewing, R. M.
Right arrow Articles by Claverie, J.-M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 9, Issue 10, 950-959, October 1999

LETTER
Large-Scale Statistical Analyses of Rice ESTs Reveal Correlated Patterns of Gene Expression

Rob M. Ewing,1 Alia Ben Kahla, Olivier Poirot, Fabrice Lopez, Stéphane Audic, and Jean-Michel Claverie

Structural and Genetic Information (SGI) Laboratory, Centre National de la Recherche Scientifique-Unité mixte de Recherche (CNRS-UMR) 1889, Marseille 13402 cedex 20, France

Large, publicly available collections of expressed sequence tags (ESTs) have been generated from Arabidopsis thaliana and rice (Oryza sativa). A potential, but relatively unexplored application of this data is in the study of plant gene expression. Other EST data, mainly from human and mouse, have been successfully used to point out genes exhibiting tissue- or disease-specific expression, as well as for identification of alternative transcripts. In this report, we go a step further in showing that computer analyses of plant EST data can be used to generate evidence of correlated expression patterns of genes across various tissues. Furthermore, tissue types and organs can be classified with respect to one another on the basis of their global gene expression patterns. As in previous studies, expression profiles are first estimated from EST counts. By clustering gene expression profiles or whole cDNA library profiles, we show that genes with similar functions, or cDNA libraries expected to share patterns of gene expression, are grouped together. Promising uses of this technique include functional genomics, in which evidence of correlated expression might complement (or substitute for) those of sequence similarity in the annotation of anonymous genes and identification of surrogate markers. The analysis presented here combines the application of a correlation-based clustering method with a graphical color map allowing intuitive visualization of patterns within a large table of expression measurements.

1   Corresponding author.

9:950-959 ©1999 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/99 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 J Exp BotHome page
A. Omid, T. Keilin, A. Glass, D. Leshkowitz, and S. Wolf
Characterization of phloem-sap transcription profile in melon plants
J. Exp. Bot., October 10, 2007; (2007) erm214v1.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. R. Malik, F. Wang, J. M. Dirpaul, N. Zhou, P. L. Polowick, A. M.R. Ferrie, and J. E. Krochko
Transcript Profiling and Identification of Molecular Markers for Early Microspore Embryogenesis in Brassica napus
Plant Physiology, May 1, 2007; 144(1): 134 - 154.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
S. H. Nagaraj, R. B. Gasser, and S. Ranganathan
A hitchhiker's guide to expressed sequence tag (EST) analysis
Brief Bioinform, January 1, 2007; 8(1): 6 - 21.
[Abstract] [Full Text] [PDF]

Home page
 J Exp BotHome page
M. Gorantla, P. Babu, V. Reddy Lachagari, A. Reddy, R. Wusirika, J. L. Bennetzen, and A. R. Reddy
Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings
J. Exp. Bot., January 1, 2007; 58(2): 253 - 265.
[Abstract] [Full Text] [PDF]

Home page
 Plant CellHome page
S. M. Brady, T. A. Long, and P. N. Benfey
Unraveling the dynamic transcriptome.
PLANT CELL, September 1, 2006; 18(9): 2101 - 2111.
[Full Text] [PDF]

Home page
 Genome Res.Home page
J. A. Udall, J. M. Swanson, K. Haller, R. A. Rapp, M. E. Sparks, J. Hatfield, Y. Yu, Y. Wu, C. Dowd, A. B. Arpat, et al.
A global assembly of cotton ESTs
Genome Res., March 1, 2006; 16(3): 441 - 450.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
F. Klimmek, A. Sjodin, C. Noutsos, D. Leister, and S. Jansson
Abundantly and Rarely Expressed Lhc Protein Genes Exhibit Distinct Regulation Patterns in Plants
Plant Physiology, March 1, 2006; 140(3): 793 - 804.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Fei, X. Tang, R. Alba, and J. Giovannoni
Tomato Expression Database (TED): a suite of data presentation and analysis tools
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D766 - D770.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
K. Kawaura, K. Mochida, and Y. Ogihara
Expression Profile of Two Storage-Protein Gene Families in Hexaploid Wheat Revealed by Large-Scale Analysis of Expressed Sequence Tags
Plant Physiology, December 1, 2005; 139(4): 1870 - 1880.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
F. Goes da Silva, A. Iandolino, F. Al-Kayal, M. C. Bohlmann, M. A. Cushman, H. Lim, A. Ergul, R. Figueroa, E. K. Kabuloglu, C. Osborne, et al.
Characterizing the Grape Transcriptome. Analysis of Expressed Sequence Tags from Multiple Vitis Species and Development of a Compendium of Gene Expression during Berry Development
Plant Physiology, October 1, 2005; 139(2): 574 - 597.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
B. Munneke, K. A. Schlauch, K. L. Simonsen, W. D. Beavis, and R. W. Doerge
Adding Confidence to Gene Expression Clustering
Genetics, August 1, 2005; 170(4): 2003 - 2011.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
X. Wu, M. G. Walker, J. Luo, and L. Wei
GBA server: EST-based digital gene expression profiling
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W673 - W676.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
C. Jantasuriyarat, M. Gowda, K. Haller, J. Hatfield, G. Lu, E. Stahlberg, B. Zhou, H. Li, H. Kim, Y. Yu, et al.
Large-Scale Identification of Expressed Sequence Tags Involved in Rice and Rice Blast Fungus Interaction
Plant Physiology, May 1, 2005; 138(1): 105 - 115.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
R. J. Wisser, Q. Sun, S. H. Hulbert, S. Kresovich, and R. J. Nelson
Identification and Characterization of Regions of the Rice Genome Associated With Broad-Spectrum, Quantitative Disease Resistance
Genetics, April 1, 2005; 169(4): 2277 - 2293.
[Abstract] [Full Text] [PDF]

Home page
 Eukaryot CellHome page
K. F. Ribichich, S. M. Salem-Izacc, R. C. Georg, R. Z. N. Vencio, L. D. Navarro, and S. L. Gomes
Gene Discovery and Expression Profile Analysis through Sequencing of Expressed Sequence Tags from Different Developmental Stages of the Chytridiomycete Blastocladiella emersonii
Eukaryot. Cell, February 1, 2005; 4(2): 455 - 464.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. H. Peng, H. Zadeh, G. R. Lazo, J. P. Gustafson, S. Chao, O. D. Anderson, L. L. Qi, B. Echalier, B. S. Gill, M. Dilbirligi, et al.
Chromosome Bin Map of Expressed Sequence Tags in Homoeologous Group 1 of Hexaploid Wheat and Homoeology With Rice and Arabidopsis
Genetics, October 1, 2004; 168(2): 609 - 623.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. G. Hossain, V. Kalavacharla, G. R. Lazo, J. Hegstad, M. J. Wentz, P. M. A. Kianian, K. Simons, S. Gehlhar, J. L. Rust, R. R. Syamala, et al.
A Chromosome Bin Map of 2148 Expressed Sequence Tag Loci of Wheat Homoeologous Group 7
Genetics, October 1, 2004; 168(2): 687 - 699.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
L. L. Qi, B. Echalier, S. Chao, G. R. Lazo, G. E. Butler, O. D. Anderson, E. D. Akhunov, J. Dvorak, A. M. Linkiewicz, A. Ratnasiri, et al.
A Chromosome Bin Map of 16,000 Expressed Sequence Tag Loci and Distribution of Genes Among the Three Genomes of Polyploid Wheat
Genetics, October 1, 2004; 168(2): 701 - 712.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
F. Sterky, R. R. Bhalerao, P. Unneberg, B. Segerman, P. Nilsson, A. M. Brunner, L. Charbonnel-Campaa, J. J. Lindvall, K. Tandre, S. H. Strauss, et al.
A Populus EST resource for plant functional genomics
PNAS, September 21, 2004; 101(38): 13951 - 13956.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
B. C. Meyers, D. W. Galbraith, T. Nelson, and V. Agrawal
Methods for Transcriptional Profiling in Plants. Be Fruitful and Replicate
Plant Physiology, June 1, 2004; 135(2): 637 - 652.
[Full Text] [PDF]

Home page
 Plant CellHome page
J. J. Giovannoni
Genetic Regulation of Fruit Development and Ripening
PLANT CELL, June 1, 2004; 16(suppl_1): S170 - S180.
[Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. W. Alkharouf and B. F. Matthews
SGMD: the Soybean Genomics and Microarray Database
Nucleic Acids Res., January 1, 2004; 32(90001): D398 - 400.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
S. Nelander, P. Mostad, and P. Lindahl
Prediction of Cell Type-Specific Gene Modules: Identification and Initial Characterization of a Core Set of Smooth Muscle-Specific Genes
Genome Res., August 1, 2003; 13(8): 1838 - 1854.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
L. Li, B. P. Brunk, J. C. Kissinger, D. Pape, K. Tang, R. H. Cole, J. Martin, T. Wylie, M. Dante, S. J. Fogarty, et al.
Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database
Genome Res., March 1, 2003; 13(3): 443 - 454.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
B. S. Watson, V. S. Asirvatham, L. Wang, and L. W. Sumner
Mapping the Proteome of Barrel Medic (Medicago truncatula)
Plant Physiology, March 1, 2003; 131(3): 1104 - 1123.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
C. M. Ronning, S. S. Stegalkina, R. A. Ascenzi, O. Bougri, A. L. Hart, T. R. Utterbach, S. E. Vanaken, S. B. Riedmuller, J. A. White, J. Cho, et al.
Comparative Analyses of Potato Expressed Sequence Tag Libraries
Plant Physiology, February 1, 2003; 131(2): 419 - 429.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. Fedorova, J. van de Mortel, P. A. Matsumoto, J. Cho, C. D. Town, K. A. VandenBosch, J. S. Gantt, and C. P. Vance
Genome-Wide Identification of Nodule-Specific Transcripts in the Model Legume Medicago truncatula
Plant Physiology, October 1, 2002; 130(2): 519 - 537.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
R. A. Prade, P. Ayoubi, S. Krishnan, S. Macwana, and H. Russell
Accumulation of Stress and Inducer-Dependent Plant-Cell-Wall-Degrading Enzymes During Asexual Development in Aspergillus nidulans
Genetics, March 1, 2001; 157(3): 957 - 967.
[Abstract] [Full Text]

Home page
 Plant Physiol.Home page
R. J. Okagaki, R. G. Kynast, S. M. Livingston, C. D. Russell, H. W. Rines, and R. L. Phillips
Mapping Maize Sequences to Chromosomes Using Oat-Maize Chromosome Addition Materials
Plant Physiology, March 1, 2001; 125(3): 1228 - 1235.
[Abstract] [Full Text]

Home page
 Plant Physiol.Home page
J. A. White, J. Todd, T. Newman, N. Focks, T. Girke, O. M. de Ilárduya, J. G. Jaworski, J. B. Ohlrogge, and C. Benning
A New Set of Arabidopsis Expressed Sequence Tags from Developing Seeds. The Metabolic Pathway from Carbohydrates to Seed Oil
Plant Physiology, December 1, 2000; 124(4): 1582 - 1594.
[Abstract] [Full Text]

Home page
 Plant Physiol.Home page
J. Fernandes, V. Brendel, X. Gai, S. Lal, V. L. Chandler, R. P. Elumalai, D. W. Galbraith, E. A. Pierson, and V. Walbot
Comparison of RNA Expression Profiles Based on Maize Expressed Sequence Tag Frequency Analysis and Micro-Array Hybridization
Plant Physiology, March 1, 2002; 128(3): 896 - 910.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.